SLC10A2 (solute carrier family 10 member 2)

Gene

• Entrez ID: 6555
• Gene name: Solute carrier family 10 member 2
• Gene symbol: SLC10A2
• Synonyms (NCBI Gene): ASBT, IBAT, ISBT, NTCP2, PBAM, PBAM1
• Chromosome: 13
• Chromosome location: 13q33.1
• Summary: This gene encodes a sodium/bile acid cotransporter. This transporter is the primary mechanism for uptake of intestinal bile acids by apical cells in the distal ileum. Bile acids are the catabolic product of cholesterol metabolism, so this protein is also

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs56398830	G>A,T	Conflicting-interpretations-of-pathogenicity, benign-likely-benign	Missense variant, coding sequence variant
rs61966074	A>G	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Missense variant, coding sequence variant
rs72547505	G>A,T	Pathogenic, uncertain-significance	Missense variant, coding sequence variant
rs112657170	G>A	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs121917848	A>G	Pathogenic	Missense variant, coding sequence variant
rs141524545	C>G,T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs150970825	G>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs190734512	A>G	Conflicting-interpretations-of-pathogenicity	Intron variant
rs199553519	C>G,T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, synonymous variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT1351621	hsa-miR-1184	CLIP-seq
MIRT1351622	hsa-miR-1237	CLIP-seq
MIRT1351623	hsa-miR-1301	CLIP-seq
MIRT1351624	hsa-miR-138	CLIP-seq
MIRT1351625	hsa-miR-186	CLIP-seq
MIRT1351626	hsa-miR-2355-3p	CLIP-seq
MIRT1351627	hsa-miR-3064-5p	CLIP-seq
MIRT1351628	hsa-miR-3133	CLIP-seq
MIRT1351629	hsa-miR-3151	CLIP-seq
MIRT1351630	hsa-miR-338-5p	CLIP-seq
MIRT1351631	hsa-miR-345	CLIP-seq
MIRT1351632	hsa-miR-3652	CLIP-seq
MIRT1351633	hsa-miR-4256	CLIP-seq
MIRT1351634	hsa-miR-4430	CLIP-seq
MIRT1351635	hsa-miR-4456	CLIP-seq
MIRT1351636	hsa-miR-4505	CLIP-seq
MIRT1351637	hsa-miR-4642	CLIP-seq
MIRT1351638	hsa-miR-4645-5p	CLIP-seq
MIRT1351639	hsa-miR-4646-3p	CLIP-seq
MIRT1351640	hsa-miR-4660	CLIP-seq
MIRT1351641	hsa-miR-4673	CLIP-seq
MIRT1351642	hsa-miR-4720-5p	CLIP-seq
MIRT1351643	hsa-miR-4799-3p	CLIP-seq
MIRT1351644	hsa-miR-5047	CLIP-seq
MIRT1351645	hsa-miR-541	CLIP-seq
MIRT1351646	hsa-miR-654-5p	CLIP-seq
MIRT1351622	hsa-miR-1237	CLIP-seq
MIRT1351624	hsa-miR-138	CLIP-seq
MIRT1351627	hsa-miR-3064-5p	CLIP-seq
MIRT1351629	hsa-miR-3151	CLIP-seq
MIRT1351631	hsa-miR-345	CLIP-seq
MIRT1351632	hsa-miR-3652	CLIP-seq
MIRT1351633	hsa-miR-4256	CLIP-seq
MIRT1351634	hsa-miR-4430	CLIP-seq
MIRT1351635	hsa-miR-4456	CLIP-seq
MIRT1351636	hsa-miR-4505	CLIP-seq
MIRT1351645	hsa-miR-541	CLIP-seq
MIRT1351646	hsa-miR-654-5p	CLIP-seq
MIRT1351621	hsa-miR-1184	CLIP-seq
MIRT1351623	hsa-miR-1301	CLIP-seq
MIRT1351626	hsa-miR-2355-3p	CLIP-seq
MIRT1351637	hsa-miR-4642	CLIP-seq
MIRT1351639	hsa-miR-4646-3p	CLIP-seq
MIRT1351640	hsa-miR-4660	CLIP-seq
MIRT1351642	hsa-miR-4720-5p	CLIP-seq
MIRT1351643	hsa-miR-4799-3p	CLIP-seq
MIRT1351644	hsa-miR-5047	CLIP-seq
MIRT2328392	hsa-miR-3120-3p	CLIP-seq
MIRT2328393	hsa-miR-3163	CLIP-seq
MIRT2328394	hsa-miR-323b-3p	CLIP-seq
MIRT2328395	hsa-miR-4310	CLIP-seq
MIRT2328396	hsa-miR-494	CLIP-seq
MIRT2328397	hsa-miR-600	CLIP-seq

Transcription factors

Transcription factor	Regulation	Reference
FOS	Repression	12454857
NR3C1	Unknown	14684580
NR5A2	Unknown	12456679

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	32296183, 33961781
GO:0005886	Component	Plasma membrane	TAS	7592981, 9109432
GO:0005902	Component	Microvillus	IEA
GO:0006811	Process	Monoatomic ion transport	IEA
GO:0006814	Process	Sodium ion transport	IEA
GO:0006869	Process	Lipid transport	IEA
GO:0008508	Function	Bile acid:sodium symporter activity	IBA
GO:0008508	Function	Bile acid:sodium symporter activity	TAS	9109432
GO:0009617	Process	Response to bacterium	IEA
GO:0015293	Function	Symporter activity	IEA
GO:0015721	Process	Bile acid and bile salt transport	IBA
GO:0015721	Process	Bile acid and bile salt transport	TAS
GO:0016020	Component	Membrane	IEA
GO:0016324	Component	Apical plasma membrane	IBA
GO:0016324	Component	Apical plasma membrane	IEA
GO:0055085	Process	Transmembrane transport	IEA

Other IDs

• MIM: 601295
• HGNC: 10906
• e!Ensembl: ENSG00000125255

Protein

• UniProt ID: Q12908
• Protein name: Ileal sodium/bile acid cotransporter (Apical sodium-dependent bile acid transporter) (ASBT) (Ileal Na(+)/bile acid cotransporter) (Ileal sodium-dependent bile acid transporter) (IBAT) (ISBT) (Na(+)-dependent ileal bile acid transporter) (Sodium/taurochola
• Protein function: Plays a critical role in the sodium-dependent reabsorption of bile acids from the lumen of the small intestine (PubMed:7592981, PubMed:9458785, PubMed:9856990). Transports various bile acids, unconjugated or conjugated, such as cholate and tauro
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF01758	SBF	39 → 220	Sodium Bile acid symporter family	Family

• Tissue specificity: TISSUE SPECIFICITY: Mainly expressed in ileum and kidney, lower expression in cecum. {ECO:0000269|PubMed:9458785}.
• Sequence:

  MNDPNSCVDNATVCSGASCVVPESNFNNILSVVLSTVLTILLALVMFSMGCNVEIKKFLG
  HIKRPWGICVGFLCQFGIMPLTGFILSVAFDILPLQAVVVLIIGCCPGGTASNILAYWVD
  GDMDLSVSMTTCSTLLALGMMPLCLLIYTKMWVDSGSIVIPYDNIGTSLVSLVVPVSIGM
  FVNHKWPQKAKIILKIGSIAGAILIVLIAVVGGILYQSAWIIAPKLWIIGTIFPVAGYSL
  GFLLARIAGLPWYRCRTVAFETGMQNTQLCSTIVQLSFTPEELNVVFTFPLIYSIFQLAF
  AAIFLGFYVAYKKCHGKNKAEIPESKENGTEPESSFYKANGGFQPDEK

• Sequence length: 348

Pathways

KEGG:

Bile secretion

Reactome:

Recycling of bile acids and salts

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
BILE ACID MALABSORPTION, PRIMARY	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bile acid malabsorption, primary, 1	Uncertain significance; Benign; Conflicting classifications of pathogenicity	ClinVar ClinVar, Disgenet, GWAS catalog, HPO ClinVar, Disgenet, GWAS catalog, HPO ClinVar, Disgenet, GWAS catalog, HPO	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Cervical cancer	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHOLELITHIASIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COGNITION DISORDERS	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COMPLICATIONS OF DIABETES MELLITUS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DELIRIUM, DEMENTIA, AMNESTIC, COGNITIVE DISORDERS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DIABETES COMPLICATIONS	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GALLSTONES	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GOUT	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INTESTINAL DISEASES	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LATE-ONSET ALZHEIMER'S DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LUNG ADENOCARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LUNG CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LUNG CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MAJOR DEPRESSIVE DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NERVOUS SYSTEM DISEASES	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NERVOUS SYSTEM DISORDER	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-MELANOMA SKIN CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PERIPHERAL ARTERIAL DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PROSTATE CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PROSTATE CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SLC10A2-related disorder	Uncertain significance; Likely benign; Benign; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SQUAMOUS CELL CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SQUAMOUS CELL LUNG CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Adenoma of large intestine	Colorectal adenoma	BEFREE	11535543, 18644122		★☆☆☆☆ Found in Text Mining only
Adenomatous Polyps	Adenomatous Polyposis	BEFREE	11535543		★☆☆☆☆ Found in Text Mining only
Alzheimer Disease	Alzheimer disease	Pubtator	27770636	Associate	★☆☆☆☆ Found in Text Mining only
Barrett Esophagus	Barrett esophagus	BEFREE	19174784, 22016432, 23687410		★☆☆☆☆ Found in Text Mining only
Barrett Esophagus	Barrett esophagus	Pubtator	19174784, 22016432, 23687410	Associate	★☆☆☆☆ Found in Text Mining only
Bile Acid Malabsorption Primary	Bile acid malabsorption	Pubtator	28898457, 34192422	Associate	★☆☆☆☆ Found in Text Mining only
Bile Acid Malabsorption, Primary	Bile Acid Malabsorption	BEFREE	9109432		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bile Acid Malabsorption, Primary	Bile Acid Malabsorption	GENOMICS_ENGLAND_DG	9109432		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bile Acid Malabsorption, Primary	Bile Acid Malabsorption	UNIPROT_DG	9109432		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bile Acid Malabsorption, Primary	Bile Acid Malabsorption	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bile Acid Malabsorption, Primary	Bile Acid Malabsorption	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bile acid synthesis defect congenital 2	Congenital bile acid synthesis defect	Pubtator	34192422	Associate	★☆☆☆☆ Found in Text Mining only
cervical cancer	Cervical Cancer	BEFREE	28351521		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangitis Sclerosing	Sclerosing cholangitis	Pubtator	28008998	Inhibit	★☆☆☆☆ Found in Text Mining only
Cholecystolithiasis	Cholecystolithiasis	BEFREE	19823678, 22093174, 23340007, 28336180, 30325047		★☆☆☆☆ Found in Text Mining only
Cholelithiasis	Cholelithiasis	BEFREE	19823678, 22093174, 22569176, 23340007, 28336180, 30325047, 30504769		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholelithiasis	Cholecystolithiasis	Pubtator	19823678	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholestasis	Cholestasis	BEFREE	14988830, 16150853, 28646179, 29080340		★☆☆☆☆ Found in Text Mining only
Cholestasis	Cholelithiasis	Pubtator	16150853	Associate	★☆☆☆☆ Found in Text Mining only
Cholestasis, progressive familial intrahepatic 1	Intrahepatic cholestasis	BEFREE	14988830, 25239307		★☆☆☆☆ Found in Text Mining only
Cognition Disorders	Cognitive disorder	CTD_human_DG	29382564		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon Carcinoma	Colon Carcinoma	BEFREE	19673539, 26210740		★☆☆☆☆ Found in Text Mining only
Colonic Neoplasms	Colonic Neoplasms	BEFREE	26210740		★☆☆☆☆ Found in Text Mining only
Colonic Neoplasms	Colonic neoplasm	Pubtator	32600423, 32788867, 33140821	Associate	★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	18644122		★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	32564470, 36890467	Associate	★☆☆☆☆ Found in Text Mining only
Crohn Disease	Crohn Disease	BEFREE	14684580, 7592981		★☆☆☆☆ Found in Text Mining only
Crohn Disease	Crohn disease	Pubtator	14684580	Inhibit	★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes Mellitus	BEFREE	20651004		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Non-Insulin-Dependent	Diabetes Mellitus	BEFREE	29304731		★☆☆☆☆ Found in Text Mining only
Diarrhea	Diarrhea	Pubtator	25239307, 34192422	Associate	★☆☆☆☆ Found in Text Mining only
Erythroblastosis, Fetal	Erythroblastosis Fetalis	BEFREE	7625077		★☆☆☆☆ Found in Text Mining only
Esophagitis	Esotropia	Pubtator	23687410	Inhibit	★☆☆☆☆ Found in Text Mining only
Familial multiple trichoepitheliomata	Multiple Trichoepithelioma	BEFREE	19174784		★☆☆☆☆ Found in Text Mining only
Fatty Liver Disease	Fatty Liver	BEFREE	27358174, 29304731, 31233523		★☆☆☆☆ Found in Text Mining only
Gallstones	Gallstones	Pubtator	16237211	Inhibit	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gallstones	Gallstones	Pubtator	19823678	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gilbert Disease (disorder)	Gilbert Disease	BEFREE	23340007		★☆☆☆☆ Found in Text Mining only
Growth Disorders	Growth disorder	Pubtator	34192422	Associate	★☆☆☆☆ Found in Text Mining only
Hypercholesterolemia	Hypercholesterolemia	BEFREE	11396803, 17470645, 28336180		★☆☆☆☆ Found in Text Mining only
Hyperlipoproteinemia Type IV	Hyperlipoproteinemia	BEFREE	10974045, 11742882		★☆☆☆☆ Found in Text Mining only
Hyperlipoproteinemia Type IV	Hyperlipoproteinemia	Pubtator	10974045	Associate	★☆☆☆☆ Found in Text Mining only
Hypertriglyceridemia	Hypertriglyceridemia	Pubtator	10974045, 29642873	Associate	★☆☆☆☆ Found in Text Mining only
Ileitis	Ileitis	BEFREE	16890608		★☆☆☆☆ Found in Text Mining only
Inflammatory Bowel Diseases	Inflammatory bowel disease	Pubtator	19487253	Associate	★☆☆☆☆ Found in Text Mining only
Intestinal Diseases	Intestinal Diseases	LHGDN	18668439		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Intrahepatic Cholestasis	Intrahepatic Cholestasis	BEFREE	11396803		★☆☆☆☆ Found in Text Mining only
Intrahepatic Cholestasis of Pregnancy	Intrahepatic cholestasis of pregnancy	Pubtator	34638773	Associate	★☆☆☆☆ Found in Text Mining only
Liver Cirrhosis Biliary	Liver cirrhosis	Pubtator	30735608	Associate	★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Lung neoplasms	Pubtator	29642873	Associate	★☆☆☆☆ Found in Text Mining only
Malabsorption Syndrome	Malabsorption Syndrome	BEFREE	30653340		★☆☆☆☆ Found in Text Mining only
Malignant tumor of colon	Colonic Neoplasms	BEFREE	19673539, 26210740		★☆☆☆☆ Found in Text Mining only
Necrotizing Enterocolitis	Necrotizing Enterocolitis	BEFREE	20616306		★☆☆☆☆ Found in Text Mining only
Necrotizing enterocolitis in fetus OR newborn	Necrotizing Enterocolitis	BEFREE	16472592, 20616306		★☆☆☆☆ Found in Text Mining only
Neonatal Alloimmune Thrombocytopenia	Alloimmune Thrombocytopenia	BEFREE	31382976		★☆☆☆☆ Found in Text Mining only
nervous system disorder	Nervous System Disorder	CTD_human_DG	21245421		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON RARE IN EUROPE: Primary bile acid malabsorption	Bile Acid Malabsorption	Orphanet			★☆☆☆☆ Found in Text Mining only
Non-alcoholic Fatty Liver Disease	Non-Alcoholic Fatty Liver Disease	BEFREE	27358174, 30096951, 30573812		★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	29642873		★☆☆☆☆ Found in Text Mining only
Nonalcoholic Steatohepatitis	Non-alcoholic Fatty Liver Disease	BEFREE	28702877, 31233523		★☆☆☆☆ Found in Text Mining only
Polyp of large intestine	Polyp Of Large Intestine	BEFREE	18644122		★☆☆☆☆ Found in Text Mining only
Primary biliary cirrhosis	Biliary Cirrhosis	BEFREE	28468009, 29704003		★☆☆☆☆ Found in Text Mining only
Primary sclerosing cholangitis	Sclerosing Cholangitis	BEFREE	29310470		★☆☆☆☆ Found in Text Mining only
Progressive intrahepatic cholestasis (disorder)	Intrahepatic Cholestasis	BEFREE	14988830		★☆☆☆☆ Found in Text Mining only
Pruritus	Pruritus	Pubtator	30735608	Associate	★☆☆☆☆ Found in Text Mining only
Steatohepatitis	Fatty Liver	BEFREE	31442319		★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	38228846	Associate	★☆☆☆☆ Found in Text Mining only